BioSimSpace.Metadynamics.CollectiveVariable.Torsion¶
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class
BioSimSpace.Metadynamics.CollectiveVariable.Torsion(atoms, hill_width=0.3500 radians, lower_bound=None, upper_bound=None, grid=None, pbc=True)¶ A class for torsion based collective variables.
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__init__(atoms, hill_width=0.3500 radians, lower_bound=None, upper_bound=None, grid=None, pbc=True)¶ Constructor.
- Parameters
atoms ([int, int, int, int]) – The indices of the four atoms involved in the torsion.
hill_width (
Angle) – The width of the Gaussian hill used to sample this variable.lower_bound (
Bound) – A lower bound on the value of the collective variable.upper_bound (
Bound) – An upper bound on the value of the collective variable.grid (
Grid) – The grid on which the collective variable will be sampled. This can help speed up long metadynamics simulations where the number of Gaussian kernels can become prohibitive.pbc (bool) – Whether to use periodic boundary conditions when computing the collective variable.
Methods
__init__(atoms[, hill_width, lower_bound, …])Constructor.
getAtoms()Return list of atom indices involved in the torsion.
getGrid()Get the grid on which the collective variable is sampled.
Return the width of the Gaussian hill used to bias this collective variable.
Get the lower bound on the collective variable.
Return whether to take account of periodic boundary conditions when computing the collective variable.
Get the upper bound on the collective variable.
Return the number of components for the collective variable.
setAtoms(atoms)Set the atoms for which the torsion will be calculated.
setGrid([grid])Set a grid on which the collective variable will be sampled.
setHillWidth(hill_width)Set the width of the Gaussian hills used to bias this collective variable.
setLowerBound([lower_bound])Set a lower bound on the value of the collective variable.
Set whether to use periodic_boundaries when calculating the collective variable.
setUpperBound([upper_bound])Set an upper bound on the value of the collective variable.
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getAtoms()¶ Return list of atom indices involved in the torsion.
- Returns
atoms – The atom indices involved in the torsion.
- Return type
[int, int, int, int]
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getGrid()¶ Get the grid on which the collective variable is sampled.
- Returns
grid – The grid on which the collective variable is sampled.
- Return type
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getHillWidth()¶ Return the width of the Gaussian hill used to bias this collective variable.
- Returns
hill_width – The width of the Gaussian hill.
- Return type
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getLowerBound()¶ Get the lower bound on the collective variable.
- Returns
lower_bound – The lower bound on the value of the collective variable.
- Return type
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getPeriodicBoundaries()¶ Return whether to take account of periodic boundary conditions when computing the collective variable.
- Returns
pbc – Whether to use periodic boundaries conditions.
- Return type
bool
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getUpperBound()¶ Get the upper bound on the collective variable.
- Returns
upper_bound – The upper bound on the value of the collective variable.
- Return type
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nComponents()¶ Return the number of components for the collective variable.
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setAtoms(atoms)¶ Set the atoms for which the torsion will be calculated. measured.
- Parameters
atoms ([int, int, int, int]) – The atoms involved in the torsion. will be measured from.
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setGrid(grid=None)¶ Set a grid on which the collective variable will be sampled. Call with no arguments to clear the grid.
- Parameters
grid (
Grid) – A grid for the collective variable.
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setHillWidth(hill_width)¶ Set the width of the Gaussian hills used to bias this collective variable.
- Parameters
hill_width (
Angle) – The width of the Gaussian hill.
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setLowerBound(lower_bound=None)¶ Set a lower bound on the value of the collective variable.
- Parameters
lower_bound (
Bound) – A lower bound on the value of the collective variable.
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setPeriodicBoundaries(pbc)¶ Set whether to use periodic_boundaries when calculating the collective variable.
- Parameters
pbc (bool) – Whether to use periodic boundaries conditions.
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